scanpy
https://github.com/scverse/scanpy
Python
Single-cell analysis in Python. Scales to >1M cells.
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- Issues
- Always add 'use_rep' for uns["neighbors"]["params"]
- Different outputs between heatmap plot and matrix expression values
- obs. vs. obs for all grouped plots using `BasePlot`
- New plot function to draw the relations between 2 categorical adata.obs variables?
- Stacked barplot
- log1p return matrix
- sc.tl.leiden, restrict_to function not properly working
- Pearson Residuals: normalization and hvg
- Performance: Investigate `pp.scale` with sparse matrices
- Start overhaul for embedding sort order
- Docs
- Python not yet supported